I don't use Vstack, so I can't help you there.
As for saving the project, as a matter of course I save each non-trivial configuration of any plug-in in a templates directory associated with each project. I do this in case I decide I want to revert to a previous config, or I want to transport a set-up to another project quickly, for example.
So, I presently have vframe files for each of the four VE VSTs I've set up, plus an .nki file for the Kontakt 2 VST, in addition to the Cubase project file.
As it happens, I expect SX3 to save the VST configs as a part of the project, and it does seem to do that fine, but perhaps because I've explicitly saved them anyway, that's having an effect on the project save/restore mechanism.
Also, I've noticed that there is a timing issue of sorts: Cubase doesn't become interactive after loading a project until all the VSTs have loaded. Previously, this meant loading all the VI instances, so they were all ready to use once you got control of Cubase back, having just finished drinking your coffee. However, now Cubase comes back before the instruments are ready, because the heavy loading is now in the external VE processes, which you still need to wait for. Could this be what you're seeing?
@Rob Elliott said:
Although my colors are way better than yours
Yikes, tone it down, I can hear them from here.